Contacts of the helix formed by residues 143 - 156 (chain K) in PDB entry 6K71
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 143 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141K LYS* 3.0 45.8 - - + +
142K TYR* 1.3 110.4 + - + +
144K ARG* 1.3 55.2 + - - +
145K PRO* 4.7 3.4 - - + -
146K GLY* 3.1 21.1 - - - +
147K TYR* 2.3 34.2 + - - +
150K TYR* 5.6 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 144 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K PHE 4.4 3.8 + - - -
9K TYR* 3.3 53.9 - - - +
38K GLU* 5.8 1.0 + - - -
101K LYS* 3.9 8.0 - - + -
142K TYR 3.2 6.7 + - - +
143K LYS* 1.3 70.5 - - - +
145K PRO* 1.3 69.4 - - + +
147K TYR* 3.2 46.2 + - - +
148K GLY* 2.8 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 145 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K LYS* 4.8 20.4 - - + +
101K LYS* 3.8 24.5 + - - +
143K LYS* 4.1 2.9 - - + -
144K ARG* 1.3 87.9 - - + +
146K GLY* 1.3 60.6 + - - +
148K GLY* 3.0 1.7 + - - -
149K ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141K LYS* 6.4 0.2 - - - -
143K LYS* 3.1 28.0 + - - +
145K PRO* 1.3 76.1 - - - +
147K TYR* 1.3 58.0 + - - +
149K ALA* 3.5 4.9 + - - +
150K TYR* 2.9 45.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K PHE 4.4 7.7 + - - -
9K TYR* 3.4 16.3 - + - -
101K LYS* 6.5 0.2 - - + -
135K ALA* 5.4 4.7 + - - +
138K PHE* 3.2 33.9 - - + +
139K ASP* 3.3 18.4 - - - -
140K ASP* 5.7 0.7 - - - -
141K LYS 5.2 7.0 - - - +
142K TYR 5.9 0.2 - - - -
143K LYS 2.3 28.5 + - - +
144K ARG* 3.2 55.8 + - - +
146K GLY* 1.3 67.6 - - - +
148K GLY* 1.3 59.1 + - - +
150K TYR* 4.2 7.8 - - + -
151K ASP* 2.8 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 148 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K LYS* 4.0 22.9 - - - -
104K LYS* 5.3 2.8 - - - +
144K ARG 2.8 14.1 + - - -
145K PRO 3.0 6.5 + - - -
147K TYR* 1.3 78.9 - - - +
149K ALA* 1.3 57.1 + - - +
151K ASP* 3.8 3.0 - - - +
152K ALA* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145K PRO 2.9 14.4 + - - +
146K GLY* 4.1 5.8 - - - +
148K GLY* 1.3 74.5 - - - +
150K TYR* 1.3 63.9 + - + +
151K ASP 3.5 0.2 - - - -
152K ALA* 3.8 8.2 - - - +
153K PHE* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K PHE 5.6 1.6 - - - +
140K ASP* 3.5 30.1 - - - +
141K LYS* 3.6 40.0 + - + +
143K LYS* 5.6 3.7 + - - -
146K GLY* 2.9 28.5 + - - +
147K TYR* 4.0 9.0 - - + +
149K ALA* 1.3 83.3 - - + +
151K ASP* 1.3 58.5 + - - +
153K PHE* 3.4 23.2 + + + +
154K LYS* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 151 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K PHE 5.4 2.8 - - - +
104K LYS* 4.8 7.0 - - + +
105K SER* 4.8 9.0 + - - -
108K VAL* 4.1 19.8 - - - +
138K PHE* 6.5 1.1 - - - -
147K TYR* 2.8 46.3 + - + +
148K GLY* 4.0 3.4 - - - +
150K TYR* 1.3 73.5 - - - +
152K ALA* 1.3 64.7 + - - +
153K PHE 3.2 0.2 - - - -
154K LYS* 3.2 44.4 + - - +
155K HIS* 4.2 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K LYS* 3.4 36.9 + - + +
148K GLY 2.9 18.2 + - - +
149K ALA* 3.8 8.3 - - - +
151K ASP* 1.3 76.9 - - - +
153K PHE* 1.3 58.7 + - - +
154K LYS 3.1 2.4 + - - -
155K HIS* 3.9 7.6 + - - +
156K ALA* 4.0 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149K ALA 2.9 20.3 + - - +
150K TYR* 3.4 27.1 - + + +
152K ALA* 1.3 74.0 - - - +
154K LYS* 1.3 62.2 + - - +
155K HIS 3.4 0.4 + - - -
156K ALA* 4.0 6.8 + - + +
159K ASP* 3.2 45.1 - - + -
160K PRO* 3.2 38.6 - - + +
162K ILE* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K VAL* 4.4 10.9 - - - +
112K LEU* 5.3 4.0 - - - +
131K PHE* 5.3 2.6 - - - -
134K THR 3.8 15.7 + - - -
135K ALA* 4.5 9.7 - - - +
138K PHE* 3.5 44.6 - - + +
150K TYR 3.1 11.6 + - - +
151K ASP* 3.2 33.2 + - - +
152K ALA 3.1 1.6 - - - -
153K PHE* 1.3 79.6 - - - +
155K HIS* 1.3 91.4 + - + +
156K ALA 3.6 0.2 - - - -
157K VAL* 4.5 6.8 - - - +
160K PRO* 4.2 12.8 - - - +
163K LEU* 5.3 4.7 - - - +
172K GLU* 5.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 155 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K LYS* 5.9 2.0 - - + -
107K THR* 6.0 0.4 - - - -
108K VAL* 3.6 32.2 - - + +
111K ILE* 3.5 34.4 - - + +
112K LEU* 4.4 13.0 - - + -
151K ASP 4.3 5.4 - - - -
152K ALA 3.9 4.6 + - - +
154K LYS* 1.3 109.1 + - + +
156K ALA* 1.3 61.6 + - - +
157K VAL* 2.8 17.4 + - - +
172K GLU* 5.0 10.3 + - - -
175K VAL* 5.6 4.5 - - + +
180K ILE* 3.9 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K ALA 4.0 14.1 + - - +
153K PHE* 4.0 6.0 + - + +
154K LYS 3.6 1.0 - - - -
155K HIS* 1.3 71.8 - - - +
157K VAL* 1.3 53.4 + - - +
158K SER 3.2 2.0 - - - -
159K ASP* 2.7 47.7 + - + +
160K PRO* 3.2 8.8 - - - +
184K LEU* 6.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il